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Massatti R, Belus MT, Dowlatshahi S, Allan GJ. Genetic analyses of Astragalus sect. Humillimi (Fabaceae) resolve taxonomy and enable effective conservation. AMERICAN JOURNAL OF BOTANY 2018; 105:1703-1711. [PMID: 30222180 DOI: 10.1002/ajb2.1157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Astragalus sect. Humillimi is distributed across the southwestern United States and contains two endangered taxa, A. cremnophylax var. cremnophylax and A. humillimus. The former was originally described from the South Rim of the Grand Canyon. Analysis of individuals discovered on the North Rim of the Grand Canyon yielded some evidence that the population represented a distinct species. To enable effective conservation, we clarify the group's taxonomy and characterize the genetic diversity of A. cremnophylax and A. humillimus. METHODS We used AFLPs to genotype most species in sect. Humillimi, focusing on the two endangered forms. We examined patterns of genetic diversity using complementary analytical approaches. KEY RESULTS Our results demonstrate that North Rim populations group with A. c. var. cremnophylax. We found low levels of genetic diversity at certain localities and strong differentiation among populations. Astragalus humillimus, which has suffered recent and severe population declines, exhibits weak differentiation among and low diversity within populations. CONCLUSIONS Our results clarify the taxonomy of sect. Humillimi and define the boundaries of A. c. var. cremnophylax, which is shown to inhabit both rims of the Grand Canyon. This clarification, and detailed analysis of genetic variation within both endangered taxa, may advance ongoing efforts to conserve these taxa. Our results suggest that range-wide genetic analysis of A. humillimus may inform recovery strategies for this taxon.
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Affiliation(s)
- Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, 86001, USA
| | - Matthew T Belus
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, 86001, USA
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Shahed Dowlatshahi
- National Park Service, Science and Resource Management Division, 17 South Entrance Rd, Grand Canyon, Arizona, 86023, USA
| | - Gerard J Allan
- Environmental Genetics & Genomics Facility, Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, 86011, USA
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Ávila-Flores IJ, Hernández-Díaz JC, González-Elizondo MS, Prieto-Ruíz JÁ, Wehenkel C. Degree of Hybridization in Seed Stands of Pinus engelmannii Carr. In the Sierra Madre Occidental, Durango, Mexico. PLoS One 2016; 11:e0152651. [PMID: 27064490 PMCID: PMC4827862 DOI: 10.1371/journal.pone.0152651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 03/17/2016] [Indexed: 11/24/2022] Open
Abstract
Hybridization is an important evolutionary force, because interspecific gene transfer can introduce more new genetic material than is directly generated by mutations. Pinus engelmannii Carr. is one of the nine most common pine species in the pine-oak forest ecoregion in the state of Durango, Mexico. This species is widely harvested for lumber and is also used in reforestation programmes. Interspecific hybrids between P.engelmannii and Pinus arizonica Engelm. have been detected by morphological analysis. The presence of hybrids in P. engelmannii seed stands may affect seed quality and reforestation success. Therefore, the goals of this research were to identify introgressive hybridization between P. engelmannii and other pine species in eight seed stands of this species in Durango, Mexico, and to examine how hybrid proportion is related to mean genetic dissimilarity between trees in these stands, using Amplified Fragment Length Polymorphism (AFLP) markers and morphological traits. Differences in the average current annual increment of putative hybrids and pure trees were also tested for statistical significance. Morphological and genetic analyses of 280 adult trees were carried out. Putative hybrids were found in all the seed stands studied. The hybrids did not differ from the pure trees in vigour or robustness. All stands with putative P. engelmannii hybrids detected by both AFLPs and morphological traits showed the highest average values of the Tanimoto distance, which indicates: i) more heterogeneous genetic material, ii) higher genetic variation and therefore iii) the higher evolutionary potential of these stands, and iv) that the morphological differentiation (hybrid/not hybrid) is strongly associated with the Tanimoto distance per stand. We conclude that natural pairwise hybrids are very common in the studied stands. Both morphological and molecular approaches are necessary to confirm the genetic identity of forest reproductive material.
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Affiliation(s)
- Israel Jaime Ávila-Flores
- Doctorado Institucional en Ciencias Agropecuarias y Forestales, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
| | - José Ciro Hernández-Díaz
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
| | - Maria Socorro González-Elizondo
- CIIDIR Unidad Durango, Instituto Politécnico Nacional, Sigma 119 Fracc, 20 de Noviembre II, Durango, Durango, México, C.P., 34220
| | - José Ángel Prieto-Ruíz
- Facultad de Ciencias Forestales, Universidad Juárez del Estado de Durango, Blv. Durango y Ave, Papaloapan s/n. Col. Valle del Sur, Durango, Durango, México, C.P., 34120
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Apdo, Postal 741, Zona Centro, Durango, Durango, México, C.P., 34000
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Veselá P, Volařík D, Mráček J. Optimization of AFLP for extremely large genomes over 70 Gb. Mol Ecol Resour 2016; 16:933-45. [PMID: 26849414 DOI: 10.1111/1755-0998.12506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 01/23/2016] [Indexed: 11/29/2022]
Abstract
Here, we present an improved amplified fragment length polymorphism (AFLP) protocol using restriction enzymes (AscI and SbfI) that recognize 8-base pair sequences to provide alternative optimization suitable for species with a genome size over 70 Gb. This cost-effective optimization massively reduces the number of amplified fragments using only +3 selective bases per primer during selective amplification. We demonstrate the effects of the number of fragments and genome size on the appearance of nonidentical comigrating fragments (size homoplasy), which has a negative impact on the informative value of AFLP genotypes. We also present various reaction conditions and their effects on reproducibility and the band intensity of the extremely large genome of Viscum album. The reproducibility of this octo-cutter protocol was calculated using several species with genome sizes ranging from 1 Gb (Carex panicea) to 76 Gb (V. album). The improved protocol also succeeded in detecting high intraspecific variability in species with large genomes (V. album, Galanthus nivalis and Pinus pumila).
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Affiliation(s)
- Petra Veselá
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Daniel Volařík
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Jaroslav Mráček
- Department of Forest Botany Dendrology and Geobiocenology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
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Thirty years of tick population genetics: A comprehensive review. INFECTION GENETICS AND EVOLUTION 2015; 29:164-79. [DOI: 10.1016/j.meegid.2014.11.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 11/22/2022]
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Whitlock R, Hipperson H, Mannarelli M, Butlin RK, Burke T. An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error. Mol Ecol Resour 2013; 8:725-35. [PMID: 21585880 DOI: 10.1111/j.1755-0998.2007.02073.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amplified fragment length polymorphism (AFLP) fingerprint data are now commonly collected using DNA sequencers. AFLP genotypes are still often scored by eye from such data - a time-consuming, error-prone and subjective process. We present a semi-automated method of genotyping sequencer-collected AFLPs at predefined fragment locations (loci) within the fingerprint. Our method uses thresholds of AFLP-polymerase chain reaction-product fluorescence intensity (peak height) in order to: (i) exclude AFLP loci that are likely to contribute high rates of error to data sets, and (ii) determine the AFLP phenotype (fragment presence or absence) at the retained loci. Error rate analysis is an integral part of this process and is used to determine optimal thresholds that minimize genotyping error, while maximizing the numbers of retained loci. We show that application of this method to a large AFLP data set allows genotype calls that are rapid, objective and repeatable, facilitating the extraction of reliable genotype data for molecular ecological studies.
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Affiliation(s)
- R Whitlock
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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Hoffman JI, Clarke A, Clark MS, Peck LS. Hierarchical population genetic structure in a direct developing antarctic marine invertebrate. PLoS One 2013; 8:e63954. [PMID: 23691125 PMCID: PMC3653801 DOI: 10.1371/journal.pone.0063954] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 04/10/2013] [Indexed: 12/02/2022] Open
Abstract
Understanding the relationship between life-history variation and population structure in marine invertebrates is not straightforward. This is particularly true of polar species due to the difficulty of obtaining samples and a paucity of genomic resources from which to develop nuclear genetic markers. Such knowledge, however, is essential for understanding how different taxa may respond to climate change in the most rapidly warming regions of the planet. We therefore used over two hundred polymorphic Amplified Fragment Length Polymorphisms (AFLPs) to explore population connectivity at three hierachical spatial scales in the direct developing Antarctic topshell Margarella antarctica. To previously published data from five populations spanning a 1500 km transect along the length of the Western Antarctic Peninsula, we added new AFLP data for four populations separated by up to 6 km within Ryder Bay, Adelaide Island. Overall, we found a nonlinear isolation-by-distance pattern, suggestive of weaker population structure within Ryder Bay than is present over larger spatial scales. Nevertheless, significantly positive Fst values were obtained in all but two of ten pairwise population comparisons within the bay following Bonferroni correction for multiple tests. This is in contrast to a previous study of the broadcast spawner Nacella concinna that found no significant genetic differences among several of the same sites. By implication, the topshell's direct-developing lifestyle may constrain its ability to disperse even over relatively small geographic scales.
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Affiliation(s)
- Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
- * E-mail:
| | - Andrew Clarke
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Melody S. Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
| | - Lloyd S. Peck
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, United Kingdom
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Ley AC, Hardy OJ. Improving AFLP analysis of large-scale patterns of genetic variation - a case study with the Central African lianasHaumaniaspp (Marantaceae) showing interspecific gene flow. Mol Ecol 2013; 22:1984-97. [DOI: 10.1111/mec.12214] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 12/06/2012] [Accepted: 12/11/2012] [Indexed: 10/27/2022]
Affiliation(s)
- A. C. Ley
- Institut für Geobotanik und Botanischer Garten; University Halle-Wittenberg; 06108 Halle (Saale) Germany
- Evolutionary Biology and Ecology; CP160/12; Faculté des Sciences; Université Libre de Bruxelles; 50 Av. F. Roosevelt 1050 Brussels Belgium
| | - O. J. Hardy
- Evolutionary Biology and Ecology; CP160/12; Faculté des Sciences; Université Libre de Bruxelles; 50 Av. F. Roosevelt 1050 Brussels Belgium
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Widespread amplification of amplified fragment length polymorphisms (AFLPs) in marine Antarctic animals. Polar Biol 2011. [DOI: 10.1007/s00300-011-1139-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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COLBECK GABRIELJ, TURGEON JULIE, SIROIS PASCAL, DODSON JULIANJ. Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus). Mol Ecol 2011; 20:1976-87. [DOI: 10.1111/j.1365-294x.2011.05069.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Paris M, Bonnes B, Ficetola GF, Poncet BN, Després L. Amplified fragment length homoplasy: in silico analysis for model and non-model species. BMC Genomics 2010; 11:287. [PMID: 20459671 PMCID: PMC2875239 DOI: 10.1186/1471-2164-11-287] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 05/07/2010] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species. RESULTS In this study we performed in silico AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti. Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species. CONCLUSIONS These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at http://www-leca.ujf-grenoble.fr/logiciels.htm.
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Affiliation(s)
- Margot Paris
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
| | - Benjamin Bonnes
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
| | - Gentile Francesco Ficetola
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
| | - Bénédicte N Poncet
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
| | - Laurence Després
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France
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Caballero A, Quesada H. Homoplasy and Distribution of AFLP Fragments: An Analysis In Silico of the Genome of Different Species. Mol Biol Evol 2010; 27:1139-51. [DOI: 10.1093/molbev/msq001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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García-Pereira MJ, Caballero A, Quesada H. Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets. Mol Biol Evol 2009; 27:988-1000. [PMID: 20026482 DOI: 10.1093/molbev/msp315] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using in silico amplified fragment length polymorphism (AFLP) fingerprints, we explore the relationship between sequence similarity and phylogeny accuracy to test when, in terms of genetic divergence, the quality of AFLP data becomes too low to be informative for a reliable phylogenetic reconstruction. We generated DNA sequences with known phylogenies using balanced and unbalanced trees with recent, uniform and ancient radiations, and average branch lengths (from the most internal node to the tip) ranging from 0.02 to 0.4 substitutions per site. The resulting sequences were used to emulate the AFLP procedure. Trees were estimated by maximum parsimony (MP), neighbor-joining (NJ), and minimum evolution (ME) methods from both DNA sequences and virtual AFLP fingerprints. The estimated trees were compared with the reference trees using a score that measures overall differences in both topology and relative branch length. As expected, the accuracy of AFLP-based phylogenies decreased dramatically in the more divergent data sets. Above a divergence of approximately 0.05, AFLP-based phylogenies were largely inaccurate irrespective of the distinct topology, radiation model, or phylogenetic method used. This value represents an upper bound of expected tree accuracy for data sets with a simple divergence history; AFLP data sets with a similar divergence but with unbalanced topologies and short ancestral branches produced much less accurate trees. The lack of homology of AFLP bands quickly increases with divergence and reaches its maximum value (100%) at a divergence of only 0.4. Low guanine-cytosine (GC) contents increase the number of nonhomologous bands in AFLP data sets and lead to less reliable trees. However, the effect of the lack of band homology on tree accuracy is surprisingly small relative to the negative impact due to the low information content of AFLP characters. Tree-building methods based on genetic distance displayed similar trends and outperformed parsimony at low but not at high divergences. However, the impact of using alternative phylogenetic methods on tree accuracy was generally small relative to the uncertainty arising from factors such as divergence, nonhomology of bands, or the low information content of AFLP characters. Nevertheless, our data suggest that under certain circumstances, AFLPs may be suitable to reconstruct deeper phylogenies than usually accepted.
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Affiliation(s)
- María Jesús García-Pereira
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidade de Vigo, Vigo, Spain
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Gort G, van Hintum T, van Eeuwijk F. Homoplasy corrected estimation of genetic similarity from AFLP bands, and the effect of the number of bands on the precision of estimation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:397-416. [PMID: 19436989 PMCID: PMC2715462 DOI: 10.1007/s00122-009-1047-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Accepted: 04/21/2009] [Indexed: 05/11/2023]
Abstract
AFLP is a DNA fingerprinting technique, resulting in binary band presence-absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50-100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce.
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Affiliation(s)
- Gerrit Gort
- Biometris, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Rowntree JK, Cowan RS, Leggett M, Ramsay MM, Fay MF. Which moss is which? Identification of the threatened moss Orthodontium gracile using molecular and morphological techniques. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9948-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wood TE, Nakazato T. Investigating species boundaries in the Giliopsis group of Ipomopsis (Polemoniaceae): Strong discordance among molecular and morphological markers. AMERICAN JOURNAL OF BOTANY 2009; 96:853-861. [PMID: 21628238 DOI: 10.3732/ajb.0800153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
As a first step in elucidating mechanisms of speciation in the Giliopsis group of Ipomopsis (Polemoniaceae), we examined patterns of morphological and genetic differentiation and crossability. This group comprises three species that diverged very recently: two perennials, I. guttata and I. tenuifolia, and one annual, I. effusa. Analysis of phenotypic variation established that the three species are distinct for floral characters, and this differentiation is maintained in a locality containing both perennial species. Next, we assessed the genealogical relationships with AFLPs. All sampled individuals of I. effusa clustered together, a result in accord with its genetic isolation. The perennials, which retain interfertility, were not resolved as sister taxa. Rather, individuals sampled from the single I. guttata population that is sympatric with I. tenuifolia were genetically more similar to I. tenuifolia samples than they were to conspecifics. This pattern may be due to substantial introgression of I. tenuifolia genomic regions that do not contribute to floral phenotype in I. guttata. Our result adds to mounting evidence that plant species, as defined by morphological characters, are often not genomically cohesive. Taken together, our data warrant caution in delimiting species with genetic markers alone, and, importantly, suggest that selection on species-diagnostic morphological characters can be sufficiently strong to counteract extensive gene flow.
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Affiliation(s)
- Troy E Wood
- Institute for Evolution and Biodiversity, Plant Evolutionary Ecology, University of Münster, Hüfferstrasse 1, Münster 48149, Germany
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Sasanuma T, Sehgal D, Sasakuma T, Raina SN. Phylogenetic analysis of Carthamus species based on the nucleotide sequence of the nuclear SACPD gene and chloroplast trnL-trnF IGS region. Genome 2008; 51:721-7. [PMID: 18772950 DOI: 10.1139/g08-059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To clarify the phylogenetic relationships of Carthamus species, we performed sequence analysis of the nuclear stearoyl acyl carrier protein desaturase (SACPD) gene and the chloroplast intergenic spacer region between leucine and phenylalanine tRNA genes (trnL-trnF IGS) in 13 taxa of Carthamus. The previous division of the genus into 4 taxonomic sections and allocation of particular genomes to various taxa on the basis of morphological, cytogenetic, and biosystematic analyses is not supported by the present study. Our results provide evidence of the occurrence of 5 nuclear genomes (A, B, C, X, and Y) and 3 cytoplasm types (A, B, and C) in the genus Carthamus. The cultivated safflower, C. tinctorius (2n = 24), has the B genome and type B cytoplasm. Both of these are not present in the polyploid taxa. This contradicts the earlier view that one of the genomes involved in the origin of the polyploid taxa of Carthamus is the B genome. Comparison with an outgroup species (Cirsium japonicum) indicated that C. arborescens is the most primitive species in the genus. Carthamus palaestinus is genetically closest to the cultivated safflower.
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Affiliation(s)
- Tsuneo Sasanuma
- Division of Evolutionary Genetics, Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan.
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Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci. Genetics 2008; 179:539-54. [PMID: 18493070 DOI: 10.1534/genetics.107.083246] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of bands with the same electrophoretic mobility, what is known as fragment-size homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP homoplasy on the estimation of within- and between-neutral population genetic diversity in a model of a structured finite population with migration among subpopulations. We also investigated the performance of a currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP homoplasy on its effectiveness. The results indicate that the biases produced by homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the band, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (up to 15-25%) may occur with approximately 50-100 fragments per primer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP homoplasy can produce a reduction of up to 15% in the power to detect selective loci.
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Gort G, Koopman WJM, Stein A, Eeuwijk FA. Collision probabilities for AFLP bands, with an application to simple measures of genetic similarity. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2008. [DOI: 10.1198/108571108x308116] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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A striking lack of genetic diversity across the wide-ranging amphibian Gastrophryne carolinensis (Anura: Microhylidae). Genetica 2008; 135:169-83. [DOI: 10.1007/s10709-008-9267-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 02/20/2008] [Indexed: 11/27/2022]
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20
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Mebert K. Good species despite massive hybridization: genetic research on the contact zone between the watersnakes Nerodia sipedon and N. fasciata in the Carolinas, USA. Mol Ecol 2008; 17:1918-29. [PMID: 18346128 DOI: 10.1111/j.1365-294x.2008.03725.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Genomic markers generated with the amplified fragment length polymorphism method revealed extensive, panmictic-like hybridization along the narrow contact zone between the water snakes Nerodia sipedon and Nerodia fasciata in the Carolinas, USA. However, asymmetric distributions of diagnostic markers between both species and low frequencies of backcrossed hybrids with a high value of interspecific mixture infer selection against certain genotypes. This is consistent with a pronounced genetic and morphological preponderance of N. fasciata characters in the hybrid zone. Despite massive hybridization within the contact zone, the existence of nearly fixed genetic markers and the potential inferiority of certain hybrid genotypes support the species status of the two taxa and corroborate known, but nondiagnostic differences in morphology and ecology. This study stretches the applicability of species concepts to cases, where the genetic compatibility between two closely related species is very high, yet, they still evolve and persist as independent entities.
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Affiliation(s)
- K Mebert
- Department of Biological Sciences, Old Dominion University, Norfolk, VA 23529, USA.
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21
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McKinnon GE, Vaillancourt RE, Steane DA, Potts BM. An AFLP marker approach to lower-level systematics in Eucalyptus (Myrtaceae). AMERICAN JOURNAL OF BOTANY 2008; 95:368-380. [PMID: 21632361 DOI: 10.3732/ajb.95.3.368] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Genus Eucalyptus, with over 700 species, presents a number of systematic difficulties including taxa that hybridize or intergrade across environmental gradients. To date, no DNA marker has been found capable of resolving phylogeny below the sectional level in the major subgenera. Molecular markers are needed to support taxonomic revision, assess the extent of genetic divergence at lower taxonomic levels, and inform conservation efforts. We examined the utility of 930 amplified fragment length polymorphisms (AFLPs) for analyzing relationships among Tasmanian taxa of subgenus Symphyomyrtus section Maidenaria. Phenetic and cladistic analyses resolved species into clusters demonstrating significant genetic partitioning, largely concordant with series defined in the most recent taxonomic revision of Eucalyptus. Some departures from current taxonomy were noted, indicating possible cases of morphological convergence and character reversion. Although the resolution obtained using AFLP was greatly superior to that of single sequence markers, the data demonstrated high homoplasy and incomplete resolution of closely related species. The results of this study and others are consistent with recent speciation and reticulate evolution in Maidenaria. We conclude that a combination of phylogenetic and population genetic approaches using multiple molecular markers offers the best prospects for understanding taxonomic relationships below the sectional level in Eucalyptus.
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22
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WHITLOCK R, HIPPERSON H, MANNARELLI M, BUTLIN RK, BURKE T. An objective, rapid and reproducible method for scoring AFLP peak-height data that minimizes genotyping error. Mol Ecol Resour 2008. [DOI: 10.1111/j.1471-8286.2007.02073.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Vallender R, Robertson RJ, Friesen VL, Lovette IJ. Complex hybridization dynamics between golden-winged and blue-winged warblers (Vermivora chrysoptera and Vermivora pinus) revealed by AFLP, microsatellite, intron and mtDNA markers. Mol Ecol 2008; 16:2017-29. [PMID: 17498229 DOI: 10.1111/j.1365-294x.2007.03282.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Blue-winged (Vermivora pinus) and golden-winged warblers (Vermivora chrysoptera) have an extensive mosaic hybrid zone in eastern North America. Over the past century, the general trajectory has been a rapid replacement of chrysoptera by pinus in a broad, northwardly moving area of contact. Previous mtDNA-based studies on these species' hybridization dynamics have yielded variable results: asymmetric and rapid introgression from pinus into chrysoptera in some areas and bidirectional maternal gene flow in others. To further explore the hybridization genetics of this otherwise well-studied complex, we surveyed variation in three nuclear DNA marker types--microsatellites, introns, and a panel of amplified fragment length polymorphisms (AFLPs)--with the goal of generating a multilocus assay of hybrid introgression. All markers were first tested on birds from phenotypically and mitochondrially pure parental-type populations from outside the hybrid zone. Searches for private alleles and assignment test approaches found no combination of microsatellite or intron markers that could separate the parental populations, but seven AFLP characters exhibited significant frequency differences among them. We then used the AFLP markers to examine the extent and pattern of introgression in a population where pinus-phenotype individuals have recently invaded a region that previously supported only a chrysoptera-phenotype population. Despite the low frequency of phenotypic hybrids at this location, the AFLP data suggest that almost a third of the phenotypically pure chrysoptera have introgressed genotypes, indicating the presence of substantial cryptic hybridization in the history of this species. The evidence for extensive cryptic introgression, combined with the lack of differentiation at other nuclear loci, cautions against hybrid assessments based on single markers or on phenotypic traits that are likely to be determined by a small number of loci. Considered in concert, these results from four classes of molecular markers indicate that pinus and chrysoptera are surprisingly weakly differentiated and that far fewer genetically 'pure' populations of chrysoptera may exist than previously assumed, two findings with broad implications for the conservation of this rapidly declining taxon.
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Affiliation(s)
- R Vallender
- Fuller Evolutionary Biology Program, Laboratory of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA.
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24
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Affiliation(s)
- H. Bradley Shaffer
- Section of Evolution and Ecology, and Center for Population Biology, University of California Davis, CA, 95616, USA E-mail: (H.B.S.) (R.C.T.)
| | - Robert C. Thomson
- Section of Evolution and Ecology, and Center for Population Biology, University of California Davis, CA, 95616, USA E-mail: (H.B.S.) (R.C.T.)
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25
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Bonin A, Ehrich D, Manel S. Statistical analysis of amplified fragment length polymorphism data: a toolbox for molecular ecologists and evolutionists. Mol Ecol 2007; 16:3737-58. [PMID: 17850542 DOI: 10.1111/j.1365-294x.2007.03435.x] [Citation(s) in RCA: 300] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recently, the amplified fragment length polymorphism (AFLP) technique has gained a lot of popularity, and is now frequently applied to a wide variety of organisms. Technical specificities of the AFLP procedure have been well documented over the years, but there is on the contrary little or scattered information about the statistical analysis of AFLPs. In this review, we describe the various methods available to handle AFLP data, focusing on four research topics at the population or individual level of analysis: (i) assessment of genetic diversity; (ii) identification of population structure; (iii) identification of hybrid individuals; and (iv) detection of markers associated with phenotypes. Two kinds of analysis methods can be distinguished, depending on whether they are based on the direct study of band presences or absences in AFLP profiles ('band-based' methods), or on allelic frequencies estimated at each locus from these profiles ('allele frequency-based' methods). We investigate the characteristics and limitations of these statistical tools; finally, we appeal for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data.
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Affiliation(s)
- A Bonin
- Diversity Arrays Technology P/L, Yarralumla, ACT 2600, Australia
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26
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Althoff DM, Gitzendanner MA, Segraves KA. The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. Syst Biol 2007; 56:477-84. [PMID: 17562471 DOI: 10.1080/10635150701427077] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The amplified fragment length polymorphism (AFLP) technique is being increasingly used in phylogenetic studies, especially in groups of rapidly radiating taxa. One of the key issues in the phylogenetic suitability of this technique is whether the DNA fragments generated via the AFLP method are homologous within and among the taxa being studied. We used a bioinformatics approach to assess homology based on both chromosomal location and sequence similarity of AFLP fragments. The AFLP technique was electronically simulated on genomes from eight organisms that represented a range of genome sizes. The results demonstrated that within a genome, the number of fragments is positively associated with genome size, and the degree of homology decreases with increasing numbers of fragments generated. The average homology of fragments was 89% for small genomes (< 400 Mb) but decreased to 59% for large genomes (> 2 Gb). Fragment homology for large genomes can be increased by excluding smaller fragments, although there is no clear upper limit for the size of fragments to exclude. A second approach is to increase the number of selective nucleotides in the final selective amplification step. For strains of the same organism, homology based on chromosome location and sequence similarity of fragments was 100%. Fragment homology for more distantly related taxa, however, decreased with greater time since divergence. We conclude that AFLP data are best suited for examining phylogeographic patterns within species and among very recently diverged species.
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Affiliation(s)
- David M Althoff
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA.
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27
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Meudt HM, Clarke AC. Almost forgotten or latest practice? AFLP applications, analyses and advances. TRENDS IN PLANT SCIENCE 2007; 12:106-17. [PMID: 17303467 DOI: 10.1016/j.tplants.2007.02.001] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 12/19/2006] [Accepted: 02/01/2007] [Indexed: 05/02/2023]
Abstract
Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR marker development. Technical advances have presented new opportunities for data analysis, and recent studies have addressed specific areas of the AFLP technique, including comparison to other genotyping methods, assessment of errors, homoplasy, phylogenetic signal and appropriate analysis techniques. Here we provide a synthesis of these areas and explore new directions for the AFLP technique in the genomic era, with the aim of providing a review that will be applicable to all AFLP-based studies.
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Affiliation(s)
- Heidi M Meudt
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
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28
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Simmons MP, Zhang LB, Webb CT, Müller K. A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference. Mol Phylogenet Evol 2007; 42:528-42. [PMID: 16997581 DOI: 10.1016/j.ympev.2006.08.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2006] [Revised: 06/30/2006] [Accepted: 08/13/2006] [Indexed: 01/27/2023]
Abstract
AFLPs (and to a lesser extent ISSRs and RAPDs) are increasingly being used for phylogenetic inference among closely related species. Presence/absence characters for each AFLP allele treat all absences as homologous to one another. With three or more alleles, terminals are grouped by their shared absence of alleles in character-based phylogenetic-inference methods in a manner that is not redundant with their shared presence of an alternative allele. We conducted simulations to quantify how severe the negative effect of using presence/absence characters of individual bands is for phylogenetic inference relative to standard multistate characters. We examined alternative tree topologies, relative branch lengths, numbers of characters, rates of evolution, and numbers of alternative alleles, using both parsimony and Nei-and-Li distance analyses. Multistate parsimony generally outperformed presence/absence parsimony, which in turn outperformed Nei-and-Li distance. Increasing the character-state space (i.e., the number of alternative character states available) was found to be advantageous for all three methods of analysis examined, but was most advantageous for multistate parsimony. However, the advantage of multistate parsimony relative to Nei-and-Li distance decreased when applied to more divergent characters. More parsimony-informative variation generally alleviated the problem associated with scoring multistate characters as presence/absence characters. The ensemble consistency index was lower for presence/absence characters relative to multistate characters.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
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29
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Wang YJ, Liu JQ, Miehe G. Phylogenetic origins of the Himalayan endemic Dolomiaea, Diplazoptilon and Xanthopappus (Asteraceae: Cardueae) based on three DNA regions. ANNALS OF BOTANY 2007; 99:311-22. [PMID: 17218340 PMCID: PMC2802998 DOI: 10.1093/aob/mcl259] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 07/04/2006] [Accepted: 10/17/2006] [Indexed: 05/12/2023]
Abstract
BACKGROUND AND AIMS It is an enduring question as to the mechanisms leading to the high diversity and the processes producing endemics with unusual morphologies in the Himalayan alpine region. In the present study, the phylogenetic relationships and origins of three such endemic genera were analysed, Dolomiaea, Diplazoptilon and Xanthopappus, all in the tribe Cardueae of Asteraceae. METHODS The nuclear rDNA internal transcribed spacer (ITS) and plastid trnL-F and psbA-trnH regions of these three genera were sequenced. The same regions for other related genera in Cardueae were also sequenced or downloaded from GenBank. Phylogenetic trees were constructed from individual and combined data sets of the three types of sequences using maximum parsimony, maximum likelihood and Bayesian analyses. KEY RESULTS The phylogenetic tree obtained allowed earlier hypotheses concerning the relationships of these three endemic genera based on gross morphology to be rejected. Frolovia and Saussurea costus were deeply nested within Dolomiaea, and the strong statistical support for the Dolomiaea-Frolovia clade suggested that circumscription of Dolomiaea should be more broadly redefined. Diplazoptilon was resolved as sister to Himalaiella, and these two together are sister to Lipschitziella. The clade comprising these three genera is sister to Jurinea, and together these four genera are sister to the Dolomiaea-Frolovia clade. Xanthopappus, previously hypothesized to be closely related to Carduus, was found to be nested within a well-supported but not fully resolved Onopordum group with Alfredia, Ancathia, Lamyropappus, Olgaea, Synurus and Syreitschikovia, rather than the Carduus group. The crude dating based on ITS sequence divergence revealed that the divergence time of Dolomiaea-Frolovia from its sister group probably occurred 13.6-12.2 million years ago (Ma), and the divergence times of the other two genera, Xanthopappus and Diplazoptilon, from their close relatives around 5.7-4.7 Ma and 2.0-1.6 Ma, respectively. CONCLUSIONS The findings provide an improved understanding of the intergeneric relationships in Cardueae. The crude calibration of lineages indicates that the uplifts of the Qiinghai-Tibetan Plateau since the Miocene might have served as a continuous stimulus for the production of these morphologically aberrant endemic elements of the Himalayan flora.
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Affiliation(s)
- Yu-Jin Wang
- Key Laboratory of Qinghai–Tibetan Plateau Ecological Adaptation, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China
- Graduate School of Chinese Academy of Sciences, Beijing 100039, China
| | - Jian-Quan Liu
- Key Laboratory of Qinghai–Tibetan Plateau Ecological Adaptation, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China
- Key Laboratory of Arid and Grassland Ecology, Lanzhou University, Lanzhou 730000, Gansu, China
| | - Georg Miehe
- Faculty of Geography, University of Marburg, Deutschhaustr. 10, D-35032 Marburg, Germany
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30
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Zhang D, Chen S, Chen S, Zhang D, Gao Q. Patterns of Genetic Variation in Swertia przewalskii, an Endangered Endemic Species of the Qinghai-Tibet Plateau. Biochem Genet 2007; 45:33-50. [PMID: 17226079 DOI: 10.1007/s10528-006-9057-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Swertia przewalskii Pissjauk. (Gentianaceae) is a critically endangered and endemic plant of the Qinghai-Tibet Plateau in China. RAPD and ISSR analyses were carried out on a total of 63 individuals to assess the extent of genetic variation in the remaining three populations. Percentage of polymorphic bands was 94% (156 bands) for RAPD and 96% (222 bands) for ISSR. A pairwise distance measure calculated from the RAPD and ISSR data was used as input for analysis of molecular variance (AMOVA). AMOVA indicated that a high proportion of the total genetic variation (52% for RAPD and 56% for ISSR) was found among populations; pairwise Phi (ST) comparisons showed that the three populations examined were significantly different (p < 0.001). Significant genetic differentiation was found based on different measures (AMOVA and Hickory theta(B)) in S. przewalskii (0.52 on RAPD and 0.56 on ISSR; 0.46 on RAPD and 0.45 on ISSR). The differentiation of the populations corresponded to low average gene flow (0.28 based on RAPD and 0.31 based on ISSR), whereas genetic distance-based clustering and coalescent-based assignment analyses revealed significant genetic isolation among populations. Our results indicate that genetic diversity is independent of population size. We conclude that although sexual reproduction and gene flow between populations of S. przewalskii are very limited, they have preserved high levels of genetic diversity. The main factors responsible for the high level of difference among populations are the isolation and recent fragmentation under human disturbance.
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Affiliation(s)
- Defang Zhang
- Laboratory of Qinghai-Tibet Biological Evolution and Adaptation, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, 59 Xiguan Avenue, Xining Qinghai 810001, PR China
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31
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Prentis PJ, White EM, Radford IJ, Lowe AJ, Clarke AR. Can hybridization cause local extinction: a case for demographic swamping of the Australian native Senecio pinnatifolius by the invasive Senecio madagascariensis? THE NEW PHYTOLOGIST 2007; 176:902-912. [PMID: 17850249 DOI: 10.1111/j.1469-8137.2007.02217.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Hybridization between native and invasive species can have several outcomes, including enhanced weediness in hybrid progeny, evolution of new hybrid lineages and decline of hybridizing species. Whether there is a decline of hybridizing species largely depends on the relative frequencies of parental taxa and the viability of hybrid progeny. Here, the individual- and population-level consequences of hybridization between the Australian native Senecio pinnatifolius and the exotic Senecio madagascariensis were investigated with amplified fragment length polymorphism (AFLP) markers, and this information was used to estimate the annual loss of viable seeds to hybridization. A high frequency (range 8.3-75.6%) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations. A hybridization advantage was observed for S. madagascariensis, where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Calculations indicated that S. pinnatifolius would produce less viable seed than S. madagascariensis, if hybridization was frequency dependent and S. madagascariensis reached a frequency of between 10 and 60%. For this native-exotic species pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. As a result of asymmetric hybridization, S. pinnatifolius would appear to be under threat if S. madagascariensis increases numerically in areas of contact.
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Affiliation(s)
- P J Prentis
- School of Natural Resource Sciences, QUT, GPO Box 2434, Brisbane 4001, Qld, Australia
- School of Environmental and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - E M White
- School of Natural Resource Sciences, QUT, GPO Box 2434, Brisbane 4001, Qld, Australia
- Alan Fletcher Research Station, Department of Natural Resources, Mines and Water and CRC for Australian Weed Management, PO Box 36, Sherwood 4075, Qld, Australia
| | - I J Radford
- Department of Environment and Conservation, PO Box 942, Kununurra, WA 6743, Australia
| | - A J Lowe
- School of Environmental and Earth Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - A R Clarke
- School of Natural Resource Sciences, QUT, GPO Box 2434, Brisbane 4001, Qld, Australia
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32
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Abstract
The bumblebee Bombus terrestris is an economically important pollinator and an emerging model species in quantitative and population genetics. We generated genetic linkage maps for 3 independent mapping populations of B. terrestris. The linkage map with the highest resolution had 21 linkage groups, which adequately represents the haploid chromosome number of B. terrestris (n = 18). This map can be considered saturated, with an average marker distance of 10.3 cM and an estimated genome coverage of 81%. Using flow cytometry, we have estimated the genome size of this species to be 625 Mb. With an estimated total recombination genome length of 2760 cM, this results in a ratio of 226 kb/cM between the physical and genetic genome sizes. A recurring set of microsatellites and amplified fragment length polymorphism (AFLP) markers allowed the alignment of 14 linkage groups between the 3 maps. We propose to adopt this core map as a reference tool for future genetic and molecular work in B. terrestris.
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Affiliation(s)
- Lena Wilfert
- ETH Zürich, Institute for Integrative Biology (IBZ), Experimental Ecology Group, ETH-Zentrum CHN, CH-8092 Zürich, Switzerland.
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Studer B, Boller B, Herrmann D, Bauer E, Posselt UK, Widmer F, Kölliker R. Genetic mapping reveals a single major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:661-71. [PMID: 16799808 DOI: 10.1007/s00122-006-0330-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Accepted: 05/27/2006] [Indexed: 05/10/2023]
Abstract
Bacterial wilt caused by Xanthomonas translucens pv. graminis (Xtg) is a major disease of economically important forage crops such as ryegrasses and fescues. Targeted breeding based on seedling inoculation has resulted in cultivars with considerable levels of resistance. However, the mechanisms of inheritance of resistance are poorly understood and further breeding progress is difficult to obtain. This study aimed to assess the relevance of the seedling screening in the glasshouse for adult plant resistance in the field and to investigate genetic control of resistance to bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.). A mapping population consisting of 306 F1 individuals was established and resistance to bacterial wilt was assessed in glasshouse and field experiments. Highly correlated data (r = 0.67-0.77, P < 0.01) between trial locations demonstrated the suitability of glasshouse screens for phenotypic selection. Analysis of quantitative trait loci (QTL) based on a high density genetic linkage map consisting of 368 amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers revealed a single major QTL on linkage group (LG) 4 explaining 67% of the total phenotypic variance (Vp). In addition, a minor QTL was observed on LG 5. Field experiments confirmed the major QTL on LG 4 to explain 43% (in 2004) to 84% (in 2005) of Vp and also revealed additional minor QTLs on LG 1, LG 4 and LG 6. The identified QTLs and the closely linked markers represent important targets for marker-assisted selection of Italian ryegrass.
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Affiliation(s)
- Bruno Studer
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstr. 191, 8046 Zurich, Switzerland
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Barrett LG, He T, Lamont BB, Krauss SL. Temporal patterns of genetic variation across a 9-year-old aerial seed bank of the shrub Banksia hookeriana (Proteaceae). Mol Ecol 2005; 14:4169-79. [PMID: 16262867 DOI: 10.1111/j.1365-294x.2005.02726.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The pattern of accumulation of genetic variation over time in seed banks is poorly understood. We examined the genetic structure of the aerial seed bank of Banksia hookeriana within a single 15-year-old population in fire-prone southwestern Australia, and compared genetic variation between adults and each year of a 9-year-old seed bank using amplified fragment length polymorphism (AFLP). B. hookeriana is well suited to the study of seed bank dynamics due to the canopy storage of its seeds, and because each annual crop can be identified. A total of 304 seeds from nine crop years and five maternal plants were genotyped, along with 113 plants from the adult population. Genetic variation, as assessed by the proportion of polymorphic markers (P(p)) and Shannon's index (I), increased slightly within the seed bank over time, while gene diversity (H(j)), did not change. P(p), I, and H(j) all indicated that genetic variation within the seed bank quickly approached the maximal level detected. Analysis of molecular variance revealed that less than 4% of variation could be accounted for by variation among seeds produced in different years, whereas there was greater differentiation among maternal plants (12.7%), and among individual seeds produced by different maternal plants (83.4%). With increasing population age, offspring generated each year were slightly more outbred, as indicated by an increase in the mean number of nonmaternal markers per offspring. There were no significant differences for H(j) or I between adults and the seed bank. Viability of seeds decreased with age, such that the viability of 9-year-old seeds was half that of 2-year-old seeds. These results suggest that variable fire frequencies have only limited potential to influence the amount of genetic variation stored within the seed bank of B. hookeriana.
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Affiliation(s)
- Luke G Barrett
- Department of Environmental Biology, Curtin University of Technology, Perth, WA 6845, Australia.
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35
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Abstract
Researchers in the field of molecular ecology and evolution require versatile and low-cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start-up time before data can be generated is often less than a week. Built-in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA-AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.
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Affiliation(s)
- Staffan Bensch
- Department of Animal Ecology, Ecology Building, Lund University, S-223 62 Lund, Sweden.
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36
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Bonin A, Pompanon F, Taberlet P. Use of amplified fragment length polymorphism (AFLP) markers in surveys of vertebrate diversity. Methods Enzymol 2005; 395:145-61. [PMID: 15865966 DOI: 10.1016/s0076-6879(05)95010-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The amplified fragment length polymorphism (AFLP) technique is one of the most informative and cost-effective fingerprinting methods. It produces polymerase chain reaction (PCR)-based multi-locus genotypes helpful in many areas of population genetics. This chapter focuses on technical laboratory information to successfully develop the AFLP technique for vertebrates. Several AFLP protocols are described, as well as recommendations about important factors of the procedure such as the choice of enzyme and primer combinations, the choice and scoring of markers, the influence of the genome size on the AFLP procedure, and the control and estimation of genotyping errors. Finally, this chapter proposes a troubleshooting guide to help resolve the main technical difficulties encountered during the AFLP procedure.
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Affiliation(s)
- Aurélie Bonin
- Laboratoire d'Ecologie Alpine, Université Joseph Fourier, F-38041 Grenoble Cedex 9, France
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37
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Abstract
AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment of fragments, (c) asymmetry in the probability of losing and gaining fragments, and (d) problems in distinguishing heterozygote from homozygote bands. In the present study, AFLP data sets of Lactuca s.l. were examined for the presence of phylogenetic signal. An indication of this signal was provided by carrying out tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA). A measure of the support for internal branches in the optimal parsimony tree (MPT) was made using bootstrap, jackknife, and decay analysis. Finally, the extent of congruence in MPTs for AFLP and internal transcribed spacer (ITS)-1 data sets for the same taxa was made using the partition homogeneity test (PHT) and the Templeton test. These analytical studies suggested the presence of phylogenetic signal in the AFLP data sets, although some incongruence was found between AFLP and ITS MPTs. An extensive literature survey undertaken indicated that authors report a general congruence of AFLP and ITS tree topologies across a wide range of taxonomic groups, suggesting that the present results and conclusions have a general bearing. In these earlier studies and those for Lactuca s.l., AFLP markers have been found to be informative at somewhat lower taxonomic levels than ITS sequences. Tentative estimates are suggested for the levels of ITS sequence divergence over which AFLP profiles are likely to be phylogenetically informative.
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Affiliation(s)
- Wim J M Koopman
- Biosystematics Group, Nationaal Herbarium Nederland-, Wageningen University branch, Wageningen University, Generaal Foulkesweg 37, 6703BL, Wageningen, The Netherlands.
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Koopman WJM, Gort G. Significance tests and weighted values for AFLP similarities, based on Arabidopsis in silico AFLP fragment length distributions. Genetics 2005; 167:1915-28. [PMID: 15342529 PMCID: PMC1471014 DOI: 10.1534/genetics.103.015693] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many AFLP studies include relatively unrelated genotypes that contribute noise to data sets instead of signal. We developed: (1) estimates of expected AFLP similarities between unrelated genotypes, (2) significance tests for AFLP similarities, enabling the detection of unrelated genotypes, and (3) weighted similarity coefficients, including band position information. Detection of unrelated genotypes and use of weighted similarity coefficients will make the analysis of AFLP data sets more informative and more reliable. Test statistics and weighted coefficients were developed for total numbers of shared bands and for Dice, Jaccard, Nei and Li, and simple matching (dis)similarity coefficients. Theoretical and in silico AFLP fragment length distributions (FLDs) were examined as a basis for the tests. The in silico AFLP FLD based on the Arabidopsis thaliana genome sequence was the most appropriate for angiosperms. The G + C content of the selective nucleotides in the in silico AFLP procedure significantly influenced the FLD. Therefore, separate test statistics were calculated for AFLP procedures with high, average, and low G + C contents in the selective nucleotides. The test statistics are generally applicable for angiosperms with a G + C content of approximately 35-40%, but represent conservative estimates for genotypes with higher G + C contents. For the latter, test statistics based on a rice genome sequence are more appropriate.
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Affiliation(s)
- Wim J M Koopman
- Nationaal Herbarium Nederland--Wageningen Branch, Biosystematics Group, Wageningen University, 6703 BL Wageningen, The Netherlands.
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39
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Papa R, Troggio M, Ajmone-Marsan P, Nonnis Marzano F. An improved protocol for the production of AFLPTM markers in complex genomes by means of capillary electrophoresis. J Anim Breed Genet 2005; 122:62-8. [PMID: 16130490 DOI: 10.1111/j.1439-0388.2004.00476.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The amplified fragment-length polymorphism (AFLP) technology is a recently introduced method to investigate genomes of different complexity, from microbial to higher organisms. It is applied to purposes as diverse as identification of species, strain and varieties, investigation of genetic diversity within and between populations, simple and complex trait mapping, and construction of linkage and physical maps. This technology has been designed on the use of primers labelled with radioactivity and on AFLP fragment separation on sequencing gel. We show that the original EcoRI/TaqI AFLP protocol does not perform appropriately when transferred to fluorescent labelling and capillary electrophoresis (CE), and propose an improved protocol for the production of high-quality AFLP markers in fish, rodents and artiodactyles by means of the Beckman-Coulter CEQ2000 automatic DNA sequencer. In addition, we describe the procedure routinely used in our laboratory to obtain binary matrices from AFLP profiles with the aid of Genographer free-share software (vers. 1.6.0, J.J. Benham, Montana State University), able to elaborate original fragment data and convert them to standard graphical formats for phylogenetic analyses. Comparison with radioactive AFLPs in goats confirmed the reliability of the protocol developed for CE. In fact, 107 fragments generated by two primer combinations and identified by both techniques were attributed the same scoring. Compared with traditional methods, the use of capillary systems and automated analysis increases data throughput and scoring reliability, decreasing the overall experimental error.
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Affiliation(s)
- R Papa
- Dipartimento di Biologia Evolutiva e Funzionale, University of Parma, Parma, Italy
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40
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He T, Krauss SL, Lamont BB, Miller BP, Enright NJ. Long-distance seed dispersal in a metapopulation of Banksia hookeriana inferred from a population allocation analysis of amplified fragment length polymorphism data. Mol Ecol 2004; 13:1099-109. [PMID: 15078448 DOI: 10.1111/j.1365-294x.2004.02120.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
There is currently a poor understanding of the nature and extent of long-distance seed dispersal, largely due to the inherent difficulty of detection. New statistical approaches and molecular markers offer the potential to accurately address this issue. A log-likelihood population allocation test (AFLPOP) was applied to a plant metapopulation to characterize interpopulation seed dispersal. Banksia hookeriana is a fire-killed shrub, restricted to sandy dune crests in fire-prone shrublands of the Eneabba sandplain, southwest Australia. Population genetic variation was assessed for 221 individuals sampled from 21 adjacent dune-crest populations of B. hookeriana using amplified fragment length polymorphism. Genetic diversity was high, with 175 of 183 (96%) amplified fragment length polymorphism markers polymorphic. Of the total genetic diversity, 8% was partitioned among populations by amova and FST. There was no relationship between genetic diversity within populations and population demographic parameters such as population size and sample size. A population allocation test on these data unambiguously assigned 177 of 221 (80.1%) individuals to a single population. Of these, 171 (77.4% of total) were assigned to the population from which they were sampled and 6 (2.7% of total) were assigned to a known population other than the one from which they were sampled. A further 9 (4.1% of total) were assigned to outside the sampled metapopulation area, and 35 individuals (15.8%) could not be assigned unambiguously to any particular population. These results suggest that both the extent [15 of 221 (6.8%) individuals originating from a population other than the one in which they occur] and distance (1.6 to > 2.5 km), of seed dispersal between dune-crest populations is greater than expected from previous studies. The extent of long-distance interpopulation seed dispersal observed provides a basis for explaining the survival of populations of the fire-killed B. hookeriana in a landscape experiencing frequent fire, where local extinctions and recolonizations may be a regular occurrence.
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Affiliation(s)
- Tianhua He
- Department of Environmental Biology, Curtin University of Technology, Perth, Australia
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41
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Wang YJ, Liu JQ. Phylogenetic analyses of Saussurea sect. Pseudoeriocoryne (Asteraceae: Cardueae) based on chloroplast DNA trnL–F sequences. BIOCHEM SYST ECOL 2004. [DOI: 10.1016/j.bse.2004.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P. How to track and assess genotyping errors in population genetics studies. Mol Ecol 2004; 13:3261-73. [PMID: 15487987 DOI: 10.1111/j.1365-294x.2004.02346.x] [Citation(s) in RCA: 775] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies.
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Affiliation(s)
- A Bonin
- Laboratoire d'Ecologie Alpine, CNRS-UMR 5553, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 09, France.
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Sullivan JP, Lavoué S, Arnegard ME, Hopkins CD. AFLPs RESOLVE PHYLOGENY AND REVEAL MITOCHONDRIAL INTROGRESSION WITHIN A SPECIES FLOCK OF AFRICAN ELECTRIC FISH (MORMYROIDEA: TELEOSTEI). Evolution 2004; 58:825-41. [PMID: 15154558 DOI: 10.1111/j.0014-3820.2004.tb00415.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Estimating species phylogeny from a single gene tree can be especially problematic for studies of species flocks in which diversification has been rapid. Here we compare a phylogenetic hypothesis derived from cytochrome b (cyt b) sequences with another based on amplified fragment length polymorphisms (AFLP) for 60 specimens of a monophyletic riverine species flock of mormyrid electric fishes collected in Gabon, west-central Africa. We analyze the aligned cyt b sequences by Wagner parsimony and AFLP data generated from 10 primer combinations using neighbor-joining from a Nei-Li distance matrix, Wagner parsimony, and Dollo parsimony. The different analysis methods yield AFLP tree topologies with few conflicting nodes. Recovered basal relationships in the group are similar between cyt b and AFLP analyses, but differ substantially at many of the more derived nodes. More of the clades recovered with the AFLP characters are consistent with the morphological characters used to designate operational taxonomic units in this group. These results support our hypothesis that the mitochondrial gene tree differs from the overall species phylogeny due at least in part to mitochondrial introgession among lineages. Mapping the two forms of electric organ found in this group onto the AFLP tree suggests that posteriorly innervated electrocytes with nonpenetrating stalks have independently evolved from anteriorly innervated, penetrating-stalk electrocytes at least three times.
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Affiliation(s)
- John P Sullivan
- Department of Neurobiology and Behavior, W263 Seeley G. Mudd Hall, Cornell University, Ithaca, New York 14853, USA.
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44
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Sullivan JP, Lavoué S, Arnegard ME, Hopkins CD. AFLPs RESOLVE PHYLOGENY AND REVEAL MITOCHONDRIAL INTROGRESSION WITHIN A SPECIES FLOCK OF AFRICAN ELECTRIC FISH (MORMYROIDEA: TELEOSTEI). Evolution 2004. [DOI: 10.1554/03-313] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Peakall R, Ebert D, Scott LJ, Meagher PF, Offord CA. Comparative genetic study confirms exceptionally low genetic variation in the ancient and endangered relictual conifer, Wollemia nobilis (Araucariaceae). Mol Ecol 2003; 12:2331-43. [PMID: 12919472 DOI: 10.1046/j.1365-294x.2003.01926.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Wollemi pine, Wollemia nobilis (Araucariaceae), was discovered in 1994 as the only extant member of the genus, previously known only from the fossil record. With fewer than 100 trees known from an inaccessible canyon in southeastern Australia, it is one of the most endangered tree species in the world. We conducted a comparative population genetic survey at allozyme, amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) loci in W. nobilis, Araucaria cunninghamii and Agathis robusta - representatives of the two sister genera. No polymorphism was detected at 13 allozyme loci, more than 800 AFLP loci or the 20 SSR loci screened in W. nobilis. In Ag. robusta only one of 12 allozyme loci, five of 800 AFLP loci and none of the 15 SSR loci were variable. For A. cunninghamii, 10 of > 800 AFLP loci and five of 20 SSR loci were variable. Thus low genetic diversity characterizes all three species. While not ruling out the existence of genetic variation, we conclude that genetic diversity is exceptionally low in the Wollemi pine. To our knowledge this is the most extreme case known in plants. We conclude that the combination of small population effects, clonality and below-average genetic variation in the family are probable contributing factors to the low diversity. The exceptionally low genetic diversity of the Wollemi pine, combined with its known susceptibility to exotic fungal pathogens, reinforces current management policies of strict control of access to the pines and secrecy of the pine locations.
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Affiliation(s)
- Rod Peakall
- School of Botany and Zoology, Australian National University, Canberra, ACT 0200, Australia.
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Vekemans X, Beauwens T, Lemaire M, Roldán-Ruiz I. Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Mol Ecol 2002; 11:139-51. [PMID: 11903911 DOI: 10.1046/j.0962-1083.2001.01415.x] [Citation(s) in RCA: 448] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We investigate the distribution of sizes of fragments obtained from the amplified fragment length polymorphism (AFLP) marker technique. We find that empirical distributions obtained in two plant species, Phaseolus lunatus and Lolium perenne, are consistent with the expected distributions obtained from analytical theory and from numerical simulations. Our results indicate that the size distribution is strongly asymmetrical, with a much higher proportion of small than large fragments, that it is not influenced by the number of selective nucleotides nor by genome size but that it may vary with genome-wide GC-content, with a higher proportion of small fragments in cases of lower GC-content when considering the standard AFLP protocol with the enzyme MseI. Results from population samples of the two plant species show that there is a negative relationship between AFLP fragment size and fragment population frequency. Monte Carlo simulations reveal that size homoplasy, arising from pulling together nonhomologous fragments of the same size, generates patterns similar to those observed in P. lunatus and L. perenne because of the asymmetry of the size distribution. We discuss the implications of these results in the context of estimating genetic diversity with AFLP markers.
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Affiliation(s)
- X Vekemans
- Université Libre de Bruxelles, Laboratoire de Génétique et Ecologie Végétales 1850 chaussée de Wavre, 1160 Bruxelles, Belgium.
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Zawko G, Krauss SL, Dixon KW, Sivasithamparam K. Conservation genetics of the rare and endangered Leucopogon obtectus (Ericaceae). Mol Ecol 2001; 10:2389-96. [PMID: 11742543 DOI: 10.1046/j.0962-1083.2001.01378.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Leucopogon obtectus Benth. is a declared rare species found in the kwongan vegetation in Western Australia. Plants on a mineral sand mine and the rehabilitation area are subject to disturbance. Genetic diversity was examined within and among all known populations using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLPs) for conservation. Both molecular markers revealed a high percentage (> 89%) of polymorphic markers and a high mean genetic distance among individuals (D = 0.3). Analysis of molecular variance showed that 86.7% (RAPD) and 89.7% (AFLP) of variability was partitioned among individuals within populations. Exact tests showed no significant population differentiation. The analyses indicated that L. obtectus exhibits high levels of genetic diversity despite small population sizes. The high levels of variability among individuals and the lack of clear population differentiation suggest that this species comprises a single, genetically diverse group. Conservation and management of L. obtectus should concentrate on maintaining the high levels of genetic variability through mixing genotypes and promoting outcrossing.
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Affiliation(s)
- G Zawko
- Botanic Gardens and Parks Authority, Kings Park and Botanic Garden, West Perth, WA 6005, Australia.
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